X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDiscoverer.java;h=02028b41acb25e5276f30cdee71f92537f1ace7a;hb=d4b1e4d0c74b1c6d0f3c3556b10be91a6aaea475;hp=40d29e7ffc9739704dc4b71d5920295bffa7991d;hpb=ae0f884be559f2f706945b379d110e9c60642364;p=jalview.git diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java index 40d29e7..02028b4 100755 --- a/src/jalview/ws/Discoverer.java +++ b/src/jalview/ws/Discoverer.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.ws; /** @@ -12,10 +30,11 @@ package jalview.ws; * @author not attributable * @version 1.0 */ +import java.util.*; + +import javax.swing.*; + import ext.vamsas.*; -import java.util.Vector; -import java.util.Hashtable; -import java.util.ArrayList; public class Discoverer extends Thread implements Runnable @@ -74,7 +93,7 @@ public class Discoverer } catch (Exception ex) { - jalview.bin.Jalview.log.error( + jalview.bin.Cache.log.error( "Serious! Service location failed\nfor URL :" + WsURL + "\n", ex); @@ -92,39 +111,89 @@ public class Discoverer public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string public static java.util.Vector serviceList = null; // flat list of services - - static + static private Vector getDiscoveryURLS() { + Vector urls = new Vector(); + String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try { - reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false); - if (reallyDiscoverServices) + StringTokenizer st = new StringTokenizer(RootServiceURLs, ","); + while (st.hasMoreElements()) { - RootServiceURL = new java.net.URL( - "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/ServiceRegistry"); - if (ServiceURLList == null) + String url = null; + try { - ServiceURLList = new Vector(); + java.net.URL u = new java.net.URL(url = st.nextToken()); + if (!urls.contains(u)) + { + urls.add(u); + } + else + { + jalview.bin.Cache.log.info( + "Ignoring duplicate url in DISCOVERY_URLS list"); + } } - if (!ServiceURLList.contains(RootServiceURL)) + catch (Exception ex) { - ServiceURLList.add(RootServiceURL); + jalview.bin.Cache.log.warn( + "Problem whilst trying to make a URL from '" + + ( (url != null) ? url : "") + "'"); + jalview.bin.Cache.log.warn( + "This was probably due to a malformed comma separated list" + + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)"); + jalview.bin.Cache.log.debug("Exception was ", ex); } } + } + catch (Exception ex) + { + jalview.bin.Cache.log.warn( + "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex); + } + if (urls.size() > 0) + { + return urls; + } + return null; + } + + /** + * fetch new services or reset to hardwired defaults depending on preferences. + */ + static public void doDiscovery() + { + jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list."); + try + { + reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false); + if (reallyDiscoverServices) + { + ServiceURLList = getDiscoveryURLS(); + } else { - jalview.bin.Jalview.log.debug("Setting default services"); + jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. - ServiceHandle[] defServices = { + ServiceHandle[] defServices = + { new ServiceHandle( "MsaWS", "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", "Muscle Multiple Protein Sequence Alignment" -), + ), + new ServiceHandle( + "MsaWS", + "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " + + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" + + " Nucleic Acids Research, 33 511-518", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", + "MAFFT Multiple Sequence Alignment"), new ServiceHandle( "MsaWS", "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + @@ -134,11 +203,12 @@ public class Discoverer "ClustalW Multiple Sequence Alignment"), new ServiceHandle( "SecStrPred", - "Cuff J. A and Barton G.J (1999) Application of enhanced " + + "Cuff J. A and Barton G.J (2000) Application of " + "multiple sequence alignment profiles to improve protein secondary structure prediction, " + "Proteins 40:502-511", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JPred Secondary Structure Prediction" - )}; + "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", + "JNet Secondary Structure Prediction" + )}; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); @@ -153,6 +223,7 @@ public class Discoverer } } + // TODO: JBPNote : make this discover more services based on list of // discovery service urls, break cyclic references to the same url and // duplicate service entries (same endpoint *and* same interface) @@ -161,15 +232,33 @@ public class Discoverer ServiceHandles shs = null; try { - jalview.bin.Jalview.log.debug("Discovering services using " + location); + jalview.bin.Cache.log.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } + catch (org.apache.axis.AxisFault f) + { + // JBPNote - should do this a better way! + if (f.getFaultReason().indexOf("(407)") > -1) + { + if (jalview.gui.Desktop.desktop != null) + { + JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window", + "Proxy Authorization Failed", + JOptionPane.WARNING_MESSAGE); + } + } + else + { + jalview.bin.Cache.log.warn("No Discovery service at " + + location); + jalview.bin.Cache.log.debug("Axis Fault", f); + } + } catch (Exception e) { - System.err.println("failed to locate Services through URL : " + - location + "\n"); - e.printStackTrace(); - + jalview.bin.Cache.log.warn("No Discovery service at " + + location); + jalview.bin.Cache.log.debug("Discovery Service General Exception", e); } if ( (shs != null) && shs.getServices().length > 0) { @@ -187,17 +276,17 @@ public class Discoverer * @return boolean */ static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat, - Hashtable sscat) + Hashtable sscat) { boolean seenNewDiscovery = false; for (int i = 0, j = sh.length; i < j; i++) { if (!cat.contains(sh[i])) { - jalview.bin.Jalview.log.debug("A " + sh[i].getAbstractName() + - " service called " + - sh[i].getName() + " exists at " + - sh[i].getEndpointURL() + "\n"); + jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + + " service called " + + sh[i].getName() + " exists at " + + sh[i].getEndpointURL() + "\n"); if (!sscat.containsKey(sh[i].getAbstractName())) { sscat.put(sh[i].getAbstractName(), cat = new Vector()); @@ -217,7 +306,7 @@ public class Discoverer disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { - jalview.bin.Jalview.log.debug( + jalview.bin.Cache.log.debug( "Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; @@ -225,7 +314,7 @@ public class Discoverer } catch (Exception e) { - jalview.bin.Jalview.log.debug( + jalview.bin.Cache.log.debug( "Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } @@ -242,9 +331,10 @@ public class Discoverer Vector cat = new Vector(); ServiceHandle sh[] = null; int s_url = 0; - if (ServiceURLList==null) + if (ServiceURLList == null) { - jalview.bin.Jalview.log.debug("No service endpoints to use for service discovery."); + jalview.bin.Cache.log.debug( + "No service endpoints to use for service discovery."); return; } while (s_url < ServiceURLList.size()) @@ -254,6 +344,13 @@ public class Discoverer buildServiceLists(sh, cat, sscat); } + else + { + jalview.bin.Cache.log.warn( + "No services at " + + ( (java.net.URL) ServiceURLList.get(s_url)) + + " - check DISCOVERY_URLS property in .jalview_properties"); + } s_url++; } // TODO: decide on correct semantics for services list - PropertyChange @@ -261,14 +358,26 @@ public class Discoverer // so no need to access original discovery thread. // Curent decision is to change properties then notify listeners with old and new values. Hashtable oldServices = services; - Vector oldServicelist = serviceList; + //Vector oldServicelist = serviceList; services = sscat; serviceList = cat; firePropertyChange("services", oldServices, services); } + /** + * creates a new thread to call discoverServices() + */ public void run() { - discoverServices(); + final Discoverer discoverer = this; + Thread discoverThread = new Thread() + { + public void run() + { + discoverer.doDiscovery(); + discoverer.discoverServices(); + } + }; + discoverThread.start(); } }